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PathBLAST specifications


Unique identifier OMICS_04886
Name PathBLAST
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained Yes

Publication for PathBLAST

PathBLAST citations


CUFID query: accurate network querying through random walk based network flow estimation

BMC Bioinformatics
PMCID: 5751815
PMID: 29297279
DOI: 10.1186/s12859-017-1899-y

[…] the well-studied species to the under-studied species). Additionally, network querying can be utilized to predict novel functional modules.Several network querying algorithms have been proposed [–]. PathBLAST [] is one of pioneering network querying algorithms, but it can search only linear pathways and the computational complexity limits the size of the query network. QPath [] can search much lo […]


Indexing a protein protein interaction network expedites network alignment

BMC Bioinformatics
PMCID: 4600321
PMID: 26453444
DOI: 10.1186/s12859-015-0756-0

[…] roblem is a related problem in the context of local alignment [, ]. It matches a small query network to a large target network to find a subnetwork in the target that is similar to the query network. PathBLAST [], TALE [], ABINET [, ] fit in this category. PathBLAST queries a simple path against a target network and returns a ranked list of matching paths and the overlaps among them in the target. […]


Systems analysis of host–parasite interactions

Wiley Interdiscip Rev Syst Biol Med
PMCID: 4679367
PMID: 26306749
DOI: 10.1002/wsbm.1311

[…] ypothetical proteins was feasible, and alternative biological functions were suggested for some annotated genes. Suthram et al. further analyzed this network using a network alignment approach called PathBLAST, an algorithm that identifies conserved pathways between organisms by identifying conserved proteins and then testing for conserved interactions. Through this, the authors found that few pro […]


GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks

Sci Rep
PMCID: 4499810
PMID: 26165520
DOI: 10.1038/srep12074

[…] tein orthology, and then incorporate network information to identify clusters of sequence-similar proteins; these clusters in the network, then, are considered putatively orthologous functional units.PathBLAST, one of the first published PPIN alignment methods, and its successor NetworkBlast, are examples of local network alignment algorithms. Both methods begin by identifying all pairs of protein […]


The post genomic era of biological network alignment

EURASIP J Bioinform Syst Biol
PMCID: 5270500
PMID: 28194172
DOI: 10.1186/s13637-015-0022-9

[…] We first discuss pairwise and then multiple local network aligners. PathBLAST [] aligns two PPI networks to identify their conserved pathways. An alignment graph is first built, in which a node represents a pair of putative orthologs (one from each network), and an ed […]


Reconstructing Genome Wide Protein–Protein Interaction Networks Using Multiple Strategies with Homologous Mapping

PLoS One
PMCID: 4300222
PMID: 25602759
DOI: 10.1371/journal.pone.0116347

[…] ese PPIs continuously grow in size, they have become increasingly useful for reconstructing PPI networks in an interesting organism.For an interesting organism, several computational methods, such as PathBlast [,] and interologs [,], have been proposed to identify PPIs through the homologs and orthologs. However, most of these methods focus on predicting PPIs in a target organism mapped from one s […]


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PathBLAST institution(s)
Whitehead Institute for Biomedical Research, Cambridge, MA, USA

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